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Ignore process selector warnings by default #2472

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merged 3 commits into from
Oct 16, 2023
Merged

Ignore process selector warnings by default #2472

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89d0271
Ignore process selector warnings unless using debug profile
fa2k Oct 16, 2023
34d47dc
Merge branch 'dev' into ignore-process-selectors
fa2k Oct 16, 2023
65af79e
Add debugging info
fa2k Oct 16, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -32,6 +32,7 @@
- Modified devcontainer permissions so that singularity can be run in Codespaces/VS Code devcontainers ([Commit a103f44](https://github.com/CarsonJM/tools/commit/a103f4484eca8c6d668e4653a4ed8d20faf1b41d))
- Update Gitpod profile resources to reflect base environment settings.
- ([#747](https://github.com/nf-core/tools/issues/747)) Add to the template the code to dump the selected pipeline parameters into a json file.
- [#2161] Disable process selector warnings by default.

### Download

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3 changes: 3 additions & 0 deletions nf_core/pipeline-template/.github/CONTRIBUTING.md
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Expand Up @@ -31,6 +31,9 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

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1 change: 1 addition & 0 deletions nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -21,6 +21,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
{%- endif %}
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
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4 changes: 4 additions & 0 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -91,6 +91,7 @@ profiles {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
Expand Down Expand Up @@ -216,6 +217,9 @@ env {
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
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No need to add this param in the global scope

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Thanks for the review!

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@fa2k fa2k Oct 16, 2023 •
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No need to add this param in the global scope

The default for this setting in nextflow is true. My idea for this is to set it to false by default [edit: this is why I used global scope], then return it to true if using debug. I can add it to a different scope, do you have a recommendation on that?

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yes, sorry I missed that it was true by default. Your code looks good then


def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
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